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r1189: fixed an out-of-memory issue

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Resolves #1166
This commit is contained in:
Heng Li
2024-03-11 10:14:20 -04:00
parent 940388f8e4
commit 0efc886012
1 changed files with 5 additions and 4 deletions
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misc/paftools.js
+5 -4
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.26-r1182-dirty';
var paftools_version = '2.26-r1189-dirty';
/*****************************
***** Library functions *****
@@ -163,7 +163,7 @@ function fasta_read(fn)
if (line[0] == ">") {
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq.toString();
h[name] = new Uint8Array(seq.buffer);
name = seq = null;
}
var m;
@@ -175,7 +175,7 @@ function fasta_read(fn)
}
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq.toString();
h[name] = new Uint8Array(seq.buffer);
}
}
buf.destroy();
@@ -188,6 +188,7 @@ function fasta_free(fa)
if (typeof k8_version == "undefined")
for (var name in fa)
fa[name].destroy();
// FIXME: for k8-1.0, sequences are not freed. This is ok for now but not general.
}
Bytes.prototype.reverse = function()
@@ -404,7 +405,7 @@ function paf_call(args)
} else if (o[1] > 0) { // shouldn't happen in theory
if (fa[o[0]] == null) throw Error('sequence "' + o[0] + '" is absent from the reference FASTA');
if (o[1] >= fa[o[0]].length) throw Error('position ' + o[1] + ' exceeds the length of sequence "' + o[0] + '"');
var ref = typeof k8_version == "undefined"? String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase() : fa[o[0]][o[1]-1].toUpperCase();
var ref = String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase();
if (o[5] == '-') // insertion
v = [o[0], o[1], '.', ref, ref + o[6].toUpperCase()];
else // deletion